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  1. Research article

    Mapping the 3D structures of small molecule binding sites

    Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan protein...

    Joshua Meyers, Nathan Brown and Julian Blagg

    Journal of Cheminformatics 2016 8:70

    Published on: 6 December 2016

  2. Methodology

    A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood

    The ability to define the regions of chemical space where a predictive model can be safely used is a necessary condition to assure the reliability of new predictions. This implies that reliability must be dete...

    Natália Aniceto, Alex A. Freitas, Andreas Bender and Taravat Ghafourian

    Journal of Cheminformatics 2016 8:69

    Published on: 3 December 2016

  3. Research Article

    Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics

    The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site o...

    Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov and Vladimir V. Poroikov

    Journal of Cheminformatics 2016 8:68

    Published on: 28 November 2016

  4. Methodology

    Programmatic conversion of crystal structures into 3D printable files using Jmol

    Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious....

    Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie and Jason E. Bara

    Journal of Cheminformatics 2016 8:66

    Published on: 23 November 2016

  5. Software

    LA-iMageS: a software for elemental distribution bioimaging using LA–ICP–MS data

    The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution im...

    Hugo López-Fernández, Gustavo de S. Pessôa, Marco A. Z. Arruda, José L. Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña and Miguel Reboiro-Jato

    Journal of Cheminformatics 2016 8:65

    Published on: 18 November 2016

  6. Methodology

    Consensus Diversity Plots: a global diversity analysis of chemical libraries

    Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinfor...

    Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen and José L. Medina-Franco

    Journal of Cheminformatics 2016 8:63

    Published on: 10 November 2016

  7. Research article

    DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitabl...

    Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic

    Journal of Cheminformatics 2016 8:64

    Published on: 10 November 2016

  8. Software

    ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

    Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, t...

    Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner and David S. Wishart

    Journal of Cheminformatics 2016 8:61

    Published on: 4 November 2016

  9. Research article

    Recognizing chemicals in patents: a comparative analysis

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER f...

    Maryam Habibi, David Luis Wiegandt, Florian Schmedding and Ulf Leser

    Journal of Cheminformatics 2016 8:59

    Published on: 28 October 2016

  10. Methodology

    Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

    In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. T...

    Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamas Kiss, Sonja Herres-Pawlis and Gabor Terstyanszky

    Journal of Cheminformatics 2016 8:58

    Published on: 20 October 2016

  11. Research article

    Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

    In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken ...

    Ludovic Chaput, Juan Martinez-Sanz, Nicolas Saettel and Liliane Mouawad

    Journal of Cheminformatics 2016 8:56

    Published on: 17 October 2016

  12. Software

    NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

    The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equal...

    Tomáš Raček, Jana Pazúriková, Radka Svobodová Vařeková, Stanislav Geidl, Aleš Křenek, Francesco Luca Falginella, Vladimír Horský, Václav Hejret and Jaroslav Koča

    Journal of Cheminformatics 2016 8:57

    Published on: 17 October 2016

  13. Research article

    Evolution of DFT studies in view of a scientometric perspective

    This bibliometric study aims to analyze the publications in which density functional theory (DFT) plays a major role. The bibliometric analysis is performed on the full publication volume of 114,138 publicatio...

    Robin Haunschild, Andreas Barth and Werner Marx

    Journal of Cheminformatics 2016 8:52

    Published on: 5 October 2016

  14. Research article

    Computational methods for prediction of in vitro effects of new chemical structures

    With a constant increase in the number of new chemicals synthesized every year, it becomes important to employ the most reliable and fast in silico screening methods to predict their safety and activity profil...

    Priyanka Banerjee, Vishal B. Siramshetty, Malgorzata N. Drwal and Robert Preissner

    Journal of Cheminformatics 2016 8:51

    Published on: 29 September 2016

  15. Software

    Jmol SMILES and Jmol SMARTS: specifications and applications

    SMILES and SMARTS are two well-defined structure matching languages that have gained wide use in cheminformatics. Jmol is a widely used open-source molecular visualization and analysis tool written in Java and...

    Robert M. Hanson

    Journal of Cheminformatics 2016 8:50

    Published on: 26 September 2016

  16. Preliminary communication

    Mixtures, metabolites, ionic liquids: a new measure to evaluate similarity between complex chemical systems

    This communication deals with the scientific problem of evaluating the similarity between two chemical systems, each described by a finite discrete set of elements/members, which are in turn p-dimensional vectors...

    Andrea Mauri, Davide Ballabio, Roberto Todeschini and Viviana Consonni

    Journal of Cheminformatics 2016 8:49

    Published on: 22 September 2016

  17. Research article

    An ensemble model of QSAR tools for regulatory risk assessment

    Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used...

    Prachi Pradeep, Richard J. Povinelli, Shannon White and Stephen J. Merrill

    Journal of Cheminformatics 2016 8:48

    Published on: 22 September 2016

  18. Database

    XMetDB: an open access database for xenobiotic metabolism

    Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly avail...

    Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. Evelo and Nina Jeliazkova

    Journal of Cheminformatics 2016 8:47

    Published on: 15 September 2016

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